I think the first two tweets are really self-explanatory. Nothing to be decrypted. They feel more like the random outbursts of someone who feels persecuted. The third is pretty self-explanatory as well. The only missing piece is what prophet they’re talking about. Assuming the tweets are all from the same ‘person,’ it must be someone from the Brotherhood. Which means if they’re talking about “them,” that they’re talking about either the people who came before or the Templars.
Since the first two tweets were talking about the Templars, I’m assuming the third is as well. As for who the Templar prophet could be, I have no idea. That tiny annoying voice in my head says “what if it’s Desmond? What if that’s the twist?” but then the bigger part of my brain bursts out laughing. I’m thinking, more realistically, it’s someone we haven’t seen before whom we’ll be introduced to in the next game(s). If it’s the leader of the Templar Order, a new one has always been introduced in each game, and I’m still waiting for part 3.2 or 3.3 to be fully Desmond in which case you’re fighting the present-day leader. That’d be cool. I’m not getting my hopes up, but I think it’d be neat.
If the tweet is talking about Juno’s crowd, then… who knows? Could be the infamous person whose bloodlines converge (whether that be Desmond or someone else, I don’t know, but I don’t think it’s Clay. I think Clay has had his story just the same as Altair and Ezio have had theirs).